Prediction method and gene signatures for the treatment of cancer

A method for treating a subject suffering from cancer, wherein the method comprises:

• a) measuring mRNA expression levels of each gene of a gene signature selected from the group consisting of:
• i) a gene signature comprising AKT2, TSC1, FKB-12, TSC2, RPTOR, RHEB, PIK3CA and PIK3CB;
• ii) a gene signature comprising KITLG and KIT;
• iii) a gene signature comprising ERK2, ARAF, CRAF, MEK1, MEK2, HRAS, ERK1, MAPK10 and KSR1;
• iv) a gene signature comprising NRG4 and NRG2;
• v) a gene signature comprising FGF10, FGF16, FGF5, FGF2 and FGF13;
• and
• vi) a gene signature comprising TLR4, PDL2, PDL1, CD16 (NK), CTLA4 and CD28;
• in a tumor sample and a histologically matched normal sample, wherein the tumor and histologically matched normal samples are both from the same subject suffering from cancer,
• b) determining if the subject is susceptible to respond to an anti-cancer therapy by:
• determining a mRNA fold change of Tumor versus Normal (Fcn TvN) for each gene of the signature,
• multiplying the Fcn TvN by expression intensity of the gene (In) in the tumor sample (In T) and/or in the normal histologically matched sample (In N) for each gene of the signature,
• determining a score based on the Fcn TvN multiplied by InT and/or In N, for the genes of the gene signature, this score being indicative of the responsiveness of the subject to the anti-cancer therapy,
• c) administering a therapeutically effective amount of the anti-cancer therapy to a subject determined responsive to the anti-cancer therapy.